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Merge pull request #134 from nf-core/release-prep
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@edmundmiller
edmundmiller authored Feb 21, 2024
2 parents 839cc85 + 7c66cbc commit b0d5bc1
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -73,7 +73,7 @@ jobs:
run: |
nf-test test \
--profile=${{ matrix.profile }} \
tests/pipeline/*.nf.test \
workflows/tests/*.nf.test \
--tap=test.tap
- uses: pcolby/tap-summary@v1
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6 changes: 5 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -3,7 +3,7 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [Unreleased]
## v2.2.0 - 2024-02-16

### Added

Expand All @@ -14,6 +14,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[#130](https://github.com/nf-core/nascent/pull/130)] - AWS Mega Tests
- [[#132](https://github.com/nf-core/nascent/pull/132)] - Add Bowtie 2 as an aligner option

### Changed

- [[#117](https://github.com/nf-core/nascent/pull/117)] - Use fromSamplesheet

## v2.1.1 - 2023-02-17

### Fixed
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4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
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@@ -1,8 +1,8 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/nascent/releases/tag/2.1.1" target="_blank">nf-core/nascent</a>
This report has been generated by the <a href="https://github.com/nf-core/nascent/releases/tag/2.2.0" target="_blank">nf-core/nascent</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/nascent/2.1.1/docs/output" target="_blank">documentation</a>.
<a href="https://nf-co.re/nascent/2.2.0/docs/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-nascent-methods-description":
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9 changes: 0 additions & 9 deletions conf/modules.config
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Expand Up @@ -18,14 +18,6 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]

withName: SAMPLESHEET_CHECK {
publishDir = [
path: { "${params.outdir}/pipeline_info" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: CUSTOM_DUMPSOFTWAREVERSIONS {
publishDir = [
path: { "${params.outdir}/pipeline_info" },
Expand Down Expand Up @@ -169,7 +161,6 @@ process {
withName: PINTS_CALLER {
// FIXME bowtie2 fails for some reason
ext.when = { params.aligner != "bowtie2" }
ext.args = { "--exp-type $params.assay_type" }
// FIXME The singularity image doesn't exist on biocontainers yet
// https://github.com/hyulab/PINTS/issues/3
ext.singularity_pull_docker_container = true
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7 changes: 7 additions & 0 deletions conf/test.config
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Expand Up @@ -32,3 +32,10 @@ params {
filter_bed = "${projectDir}/tests/config/unwanted_region.bed"
intersect_bed = "${projectDir}/tests/config/wanted_region.bed"
}

process {
withName: 'PINTS_CALLER' {
// HACK Tests fail after latest modules update
ext.args = { "--disable-small" }
}
}
73 changes: 37 additions & 36 deletions modules.json
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Expand Up @@ -7,27 +7,27 @@
"nf-core": {
"bbmap/pileup": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": ["modules"]
},
"bedtools/genomecov": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": ["modules"]
},
"bedtools/intersect": {
"branch": "master",
"git_sha": "e576ba52f6babb06cd7946c286e5bb4f494ee02c",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": ["modules"]
},
"bedtools/merge": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": ["modules"]
},
"bedtools/sort": {
"branch": "master",
"git_sha": "f1f473b21811b958d1317c4a97c56e16d3ee40f9",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": ["modules"]
},
"bowtie2/align": {
Expand All @@ -42,37 +42,37 @@
},
"bwa/index": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"bwa/mem": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "1e2b7fb7106852388610c0360d234b0829eb980e",
"installed_by": ["fastq_align_bwa", "modules"]
},
"bwamem2/index": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"bwamem2/mem": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "1e2b7fb7106852388610c0360d234b0829eb980e",
"installed_by": ["modules"]
},
"cat/cat": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "81f27e75847087865299cc46605deb3b09b4e0a2",
"installed_by": ["modules"]
},
"cat/fastq": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "02fd5bd7275abad27aad32d5c852e0a9b1b98882",
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
"git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1",
"installed_by": ["modules"]
},
"custom/getchromsizes": {
Expand All @@ -82,28 +82,28 @@
},
"deeptools/bamcoverage": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"dragmap/align": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde",
"installed_by": ["modules"],
"patch": "modules/nf-core/dragmap/align/dragmap-align.diff"
},
"dragmap/hashtable": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"fastp": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "003920c7f9a8ae19b69a97171922880220bedf56",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9",
"git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
"installed_by": ["modules"]
},
"gffread": {
Expand Down Expand Up @@ -138,77 +138,78 @@
},
"multiqc": {
"branch": "master",
"git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
"git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290",
"installed_by": ["modules"]
},
"pints/caller": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": ["modules"],
"patch": "modules/nf-core/pints/caller/pints-caller.diff"
},
"preseq/ccurve": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": ["modules"]
},
"preseq/lcextrap": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "9a88058962c0ee1715f2ad0e017c37e0cd75e532",
"installed_by": ["modules"]
},
"rseqc/inferexperiment": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "41f4baa439663b9027727d83a3293db93bad3f8c",
"installed_by": ["modules"]
},
"rseqc/readdistribution": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "d5f5ce9474983fe0973b26c39728b5c57b13c8d4",
"installed_by": ["modules"]
},
"rseqc/readduplication": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "41f4baa439663b9027727d83a3293db93bad3f8c",
"installed_by": ["modules"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_stats_samtools"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_stats_samtools"]
},
"samtools/index": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_dedup_stats_samtools_umitools", "bam_sort_stats_samtools"]
},
"samtools/sort": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_sort_stats_samtools"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_stats_samtools"]
},
"subread/featurecounts": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "f6bba1a67cdbb605f24d7a4e8dd383b0eec45b52",
"installed_by": ["modules"]
},
"umitools/dedup": {
"branch": "master",
"git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
"git_sha": "ff7e93715a2acecf3f143ec78c9858deba2984d0",
"installed_by": ["bam_dedup_stats_samtools_umitools"]
},
"untar": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
"installed_by": ["modules"]
}
}
Expand All @@ -217,17 +218,17 @@
"nf-core": {
"bam_dedup_stats_samtools_umitools": {
"branch": "master",
"git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["subworkflows"]
},
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["fastq_align_bowtie2", "fastq_align_bwa", "subworkflows"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_dedup_stats_samtools_umitools", "bam_sort_stats_samtools", "subworkflows"]
},
"fastq_align_bowtie2": {
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1 change: 0 additions & 1 deletion ...ules/local/grohmm/parametertuning.nf.test → ...grohmm/parametertuning/tests/main.nf.test
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Expand Up @@ -29,7 +29,6 @@ nextflow_process {
then {
// FIXME Broken test
assert process.failed
assert snapshot(process.out).match()
}

}
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1 change: 0 additions & 1 deletion ...es/local/grohmm/transcriptcalling.nf.test → ...ohmm/transcriptcalling/tests/main.nf.test
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Expand Up @@ -29,7 +29,6 @@ nextflow_process {
then {
// FIXME Broken test
assert process.failed
assert snapshot(process.out).match()
}

}
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2 changes: 1 addition & 1 deletion modules/local/gtf2bed.nf
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Expand Up @@ -5,7 +5,7 @@ process GTF2BED {
conda "conda-forge::perl=5.26.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/perl:5.26.2' :
'quay.io/biocontainers/perl:5.26.2' }"
'biocontainers/perl:5.26.2' }"

input:
path gtf
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2 changes: 1 addition & 1 deletion modules/local/gtf_gene_filter.nf
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Expand Up @@ -5,7 +5,7 @@ process GTF_GENE_FILTER {
conda "conda-forge::python=3.8.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/python:3.8.3' :
'quay.io/biocontainers/python:3.8.3' }"
'biocontainers/python:3.8.3' }"

input:
path fasta
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9 changes: 9 additions & 0 deletions modules/nf-core/bbmap/pileup/environment.yml
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4 changes: 2 additions & 2 deletions modules/nf-core/bbmap/pileup/main.nf
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8 changes: 3 additions & 5 deletions modules/nf-core/bbmap/pileup/meta.yml
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7 changes: 7 additions & 0 deletions modules/nf-core/bedtools/genomecov/environment.yml
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